RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa L.) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, for the first time we have successfully generated in vivo Structure-seq libraries in rice. We found that the structural flexibility of mRNAs might associate with the dynamics of biological function. Higher N6-methyladenosine (m6A) modification tends to have less RNA structure in 3’UTR. GC content does not significantly affect in vivo mRNA structure to maintain efficient biological processes such as translation. Comparative analysis of RNA structurome between rice and Arabidopsis revealed that higher GC content does not lead to stronger structure and less RNA structural flexibility. We also found a weak correlation between sequence and structure conservation of the orthologs between rice and Arabidopsis. The conservation and divergence of both sequence and in vivo RNA structure corresponds to diverse and specific biological processes. Our results indicate that RNA secondary structure might offer a separate layer of selection to sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently for various biological processes to maintain robustness in development and flexibility in adaptation during angiosperm evolution.